Contacts of the helix formed by residues 67 - 87 (chain K) in PDB entry 4GGF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 67 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C THR* 5.3 7.9 - - + -
81C MET* 3.5 20.4 - - - +
85C ARG* 3.6 13.3 - - - +
16K TYR* 3.2 11.4 - - - -
27K HIS* 3.3 17.3 - - + +
61K ASN* 5.5 0.6 + - - +
63K ASP* 5.7 2.2 + - - +
65K ALA 3.8 1.0 - - - -
66K VAL* 1.3 72.4 - - - +
68K PHE* 1.3 62.2 + - - +
69K GLN* 3.1 36.9 + - - +
70K GLU* 2.7 38.7 + - - +
71K PHE* 3.0 21.3 + - - +
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Residues in contact with PHE 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K ILE* 3.8 21.5 - - + -
16K TYR* 3.4 43.7 + + + -
17K HIS* 5.0 0.9 - + - -
27K HIS* 4.4 6.0 + - + +
67K ASN* 1.3 77.7 - - - +
69K GLN* 1.3 58.8 + - - +
71K PHE* 3.2 23.2 + + - +
72K LEU* 3.1 43.2 + - + +
87L THR* 3.7 29.8 - - + -
88L TRP* 3.7 23.3 - + + -
91L HIS* 3.8 38.8 - - + +
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Residues in contact with GLN 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C MET* 4.0 17.7 + - + +
84C ALA* 6.1 1.2 - - - +
85C ARG* 3.1 38.2 + - - +
67K ASN* 3.1 33.6 + - - +
68K PHE* 1.3 75.9 + - - +
70K GLU* 1.3 66.8 + - + +
72K LEU* 3.2 20.1 + - + +
73K ILE* 3.6 9.1 + - - +
88L TRP* 3.3 38.4 - - + -
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Residues in contact with GLU 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C MET* 3.9 8.6 - - + +
58K LEU* 3.2 33.1 - - - +
60K ILE* 3.0 27.1 + - + +
61K ASN* 3.0 12.6 + - - +
65K ALA 3.1 3.1 - - - +
66K VAL* 3.8 9.0 - - + -
67K ASN* 2.7 47.6 + - - +
69K GLN* 1.3 76.0 - - + +
71K PHE* 1.3 65.7 + - - +
73K ILE* 3.0 27.5 + - - +
102K CA 2.4 32.1 - - - -
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Residues in contact with PHE 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ILE* 3.8 22.2 - - + -
15K VAL* 4.5 3.1 - - + -
16K TYR* 3.4 48.5 - + + -
34K LEU* 6.0 0.7 - - + -
37K LEU* 4.0 28.0 - - + -
58K LEU* 5.3 0.4 - - + -
66K VAL* 3.6 11.1 - - + +
67K ASN 3.0 14.0 + - - +
68K PHE* 3.2 19.0 + + - +
70K GLU* 1.3 75.6 - - - +
72K LEU* 1.3 66.9 + - + +
74K LEU* 3.1 32.7 + - + +
75K VAL* 3.1 34.6 + - + +
8L LEU* 4.4 15.5 - - + -
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Residues in contact with LEU 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ILE* 4.6 2.9 - - + -
68K PHE* 3.1 44.0 + - + +
69K GLN* 3.5 10.8 - - + +
70K GLU 3.2 1.0 - - - -
71K PHE* 1.3 77.4 - - + +
73K ILE* 1.3 56.8 + - - +
75K VAL* 3.6 22.0 - - + +
76K ILE* 2.9 35.6 + - + +
84L ALA* 3.8 34.5 - - + +
87L THR* 4.1 24.0 - - + -
88L TRP* 4.0 18.2 - - + +
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Residues in contact with ILE 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ILE* 3.7 33.7 - - + -
73A ILE* 4.5 12.8 - - + -
58K LEU* 3.7 9.9 - - + +
60K ILE* 3.4 37.2 - - + -
69K GLN 3.6 7.7 + - - +
70K GLU* 3.0 18.7 + - - +
72K LEU* 1.3 77.9 - - - +
74K LEU* 1.3 63.1 + - - +
76K ILE* 3.4 3.3 + - + +
77K LYS* 3.0 31.7 + - + +
103K GOL 3.6 22.2 - - - +
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Residues in contact with LEU 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K LEU* 5.0 2.0 - - + -
37K LEU* 4.0 26.9 - - + -
38K LEU* 4.1 12.8 - - + -
46K ILE* 4.2 5.4 - - + -
54K TRP* 3.7 40.8 - - + -
58K LEU* 3.7 27.0 - - + +
71K PHE* 3.1 23.5 + - + +
73K ILE* 1.3 79.9 - - - +
75K VAL* 1.3 57.3 + - - +
77K LYS* 3.3 3.9 + - - -
78K MET* 2.8 58.5 + - + +
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Residues in contact with VAL 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ILE* 4.0 32.8 - - + -
71K PHE* 3.1 48.4 + - + +
72K LEU* 3.6 16.4 - - + +
73K ILE 3.3 0.2 - - - -
74K LEU* 1.3 77.4 - - - +
76K ILE* 1.3 58.2 + - + +
78K MET* 3.4 7.0 + - - +
79K GLY* 2.9 26.0 + - - -
8L LEU* 4.4 7.4 - - + -
12L ILE* 4.2 12.8 - - + +
15L ILE* 5.6 3.1 - - + -
80L ILE* 4.3 6.4 - - + +
84L ALA* 6.3 2.2 - - + -
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Residues in contact with ILE 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ILE* 3.7 35.4 - - + +
61A ASN* 3.7 21.3 - - + -
72K LEU* 2.9 24.8 + - + +
73K ILE* 3.7 4.9 - - + +
75K VAL* 1.3 76.6 - - + +
77K LYS* 1.3 61.6 + - - +
79K GLY* 3.2 2.3 + - - -
80K VAL* 3.0 23.2 + - - +
80L ILE* 3.9 20.4 - - + +
81L MET* 3.8 24.2 - - + -
84L ALA* 3.8 26.9 - - + -
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Residues in contact with LYS 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS 5.3 5.0 + - - -
57A GLU* 5.1 3.0 + - - +
59A ASP 5.4 1.3 - - - -
60A ILE* 3.6 36.6 - - + +
62A THR* 6.2 2.0 - - - -
46K ILE* 4.9 2.6 - - + +
49K LYS* 5.3 2.1 - - - +
54K TRP* 4.1 29.4 - - + -
57K GLU* 4.3 9.3 + - - -
73K ILE* 3.0 27.7 + - + +
74K LEU 3.7 3.4 - - - +
76K ILE* 1.3 75.9 - - - +
78K MET* 1.3 63.5 + - - +
80K VAL* 3.4 4.7 + - - +
81K ALA* 3.0 25.3 + - - +
103K GOL 3.7 22.8 - - - -
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Residues in contact with MET 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K GLU 4.0 8.5 - - - +
42K SER* 4.1 11.2 - - - -
43K PRO* 3.9 25.6 - - + -
45K TYR* 4.6 1.9 + - - -
46K ILE* 4.1 22.0 - - + -
74K LEU* 2.8 48.6 + - + +
75K VAL* 3.6 1.8 - - - +
77K LYS* 1.3 72.5 - - - +
79K GLY* 1.3 57.4 + - - +
81K ALA* 3.4 1.6 + - - +
82K ALA* 2.9 31.0 + - - +
8L LEU* 3.8 28.9 - - + -
9L GLU* 4.6 5.8 - - + -
12L ILE* 3.5 26.6 - - + +
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Residues in contact with GLY 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K VAL 2.9 11.4 + - - -
76K ILE 3.2 3.6 + - - -
78K MET* 1.3 73.5 - - - +
80K VAL* 1.3 65.8 + - - +
82K ALA* 3.3 1.4 + - - +
83K HIS* 3.0 19.6 + - - +
12L ILE* 3.8 19.2 - - - +
16L ILE* 4.0 1.0 - - - +
76L PHE* 3.4 15.8 - - - -
80L ILE* 3.7 15.9 - - - -
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Residues in contact with VAL 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ILE 5.7 0.7 - - - +
61A ASN* 3.9 23.1 - - - +
62A THR* 3.6 20.2 - - - +
76K ILE 3.0 17.1 + - - +
77K LYS* 4.0 5.6 - - - +
79K GLY* 1.3 76.0 - - - +
81K ALA* 1.3 58.9 + - - +
83K HIS* 3.3 3.3 + - - +
84K LYS* 3.0 30.4 + - + +
76L PHE* 4.2 8.3 - - + -
77L GLU* 4.0 25.7 - - + +
80L ILE* 4.1 19.3 - - + -
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Residues in contact with ALA 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K TYR* 3.9 24.5 - - + -
46K ILE* 4.5 6.7 - - + -
77K LYS 3.0 18.4 + - - +
78K MET 3.8 4.0 - - - +
80K VAL* 1.3 78.6 - - - +
82K ALA* 1.3 62.1 + - - +
84K LYS* 3.2 9.7 + - - +
85K LYS* 3.0 28.7 + - - +
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Residues in contact with ALA 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K TYR* 3.8 15.6 + - - +
78K MET 2.9 19.0 + - - +
79K GLY 3.8 0.4 - - - +
81K ALA* 1.3 77.8 - - - +
83K HIS* 1.3 56.2 + - - +
85K LYS* 3.3 5.8 + - - +
86K SER* 3.0 28.6 + - - -
12L ILE* 4.0 11.0 - - + -
16L ILE* 3.6 19.6 - - + +
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Residues in contact with HIS 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K GLY 3.0 11.5 + - - +
80K VAL 3.7 4.2 + - - +
82K ALA* 1.3 75.3 - - - +
84K LYS* 1.3 66.6 + - - +
86K SER* 2.8 22.5 + - - -
87K HIS* 3.5 12.9 - + - -
16L ILE* 3.4 12.1 - - + +
20L HIS* 3.5 15.9 - + - -
30L ASP* 3.1 12.4 + - - -
76L PHE* 3.4 57.7 - + + +
77L GLU* 4.7 13.6 + - - -
201L MN 2.1 36.1 + - - -
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Residues in contact with LYS 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K VAL* 3.0 17.0 + - + +
81K ALA* 3.2 10.7 + - - +
83K HIS* 1.3 82.3 + - - +
85K LYS* 1.3 62.2 + - + +
87K HIS* 3.1 17.3 + - - +
88K GLU* 3.5 32.3 - - + +
77L GLU* 5.9 2.0 - - - +
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Residues in contact with LYS 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K TYR* 3.5 63.7 - - + +
81K ALA* 3.0 15.4 + - - +
82K ALA* 3.8 6.3 - - - +
83K HIS 3.2 0.2 - - - -
84K LYS* 1.3 72.4 - - + +
86K SER* 1.3 63.0 + - - +
87K HIS 3.0 5.6 - - - -
88K GLU* 3.0 42.5 + - + +
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Residues in contact with SER 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K ALA 3.0 13.7 + - - -
83K HIS* 2.8 20.9 + - - -
85K LYS* 1.3 77.2 - - - +
87K HIS* 1.3 63.9 + - - +
88K GLU 3.4 2.5 + - - +
16L ILE* 4.6 11.2 - - - -
20L HIS* 3.6 23.2 - - - -
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Residues in contact with HIS 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K HIS* 3.5 25.6 - + - -
84K LYS* 3.1 9.2 + - - +
85K LYS 3.0 1.0 - - - -
86K SER* 1.3 83.3 + - - +
88K GLU* 1.3 61.1 + - - +
89K GLU 4.4 0.2 + - - -
20L HIS* 3.0 17.3 + + - -
30L ASP* 3.6 10.3 - - + -
201L MN 2.0 37.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il